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  The PRIDE database and related tools and resources in 2019: improving support for quantification data

Perez-Riverol, Y., Csordas, A., Bai, J., Bernal-Llinares, M., Hewapathirana, S., Kundu, D. J., et al. (2019). The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Research, 47(D1), D442-D450. doi:10.1093/nar/gky1106.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0003-CA96-0 Version Permalink: http://hdl.handle.net/21.11116/0000-0003-CA97-F
Genre: Journal Article

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 Creators:
Perez-Riverol, Yasset1, Author
Csordas, Attila1, Author
Bai, Jingwen1, Author
Bernal-Llinares, Manuel1, Author
Hewapathirana, Suresh1, Author
Kundu, Deepti J.1, Author
Inuganti, Avinash1, Author
Griss, Johannes1, Author
Mayer, Gerhard1, Author
Eisenacher, Martin1, Author
Perez, Enrique1, Author
Uszkoreit, Julian1, Author
Pfeuffer, Julianus1, Author
Sachsenberg, Timo1, Author
Yilmaz, Sule2, Author              
Tiwary, Shivani2, Author              
Cox, Jürgen2, Author              
Audain, Enrique1, Author
Walzer, Mathias1, Author
Jarnuczak, Andrew F.1, Author
Ternent, Tobias1, AuthorBrazma, Alvis1, AuthorVizcaino, Juan Antonio1, Author more..
Affiliations:
1external, ou_persistent22              
2Cox, Jürgen / Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Max Planck Society, ou_2063284              

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Free keywords: PROTEIN IDENTIFICATION; PROTEOMICS DATA; PROTEOMEXCHANGE; PLATFORM; VISUALIZATION; PEPTIDEATLAS; MULTIPLE; UPDATEBiochemistry & Molecular Biology;
 Abstract: The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's largest data repository of mass spectrometry-based proteomics data, and is one of the founding members of the global ProteomeXchange (PX) consortium. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2016. In the last 3years, public data sharing through PRIDE (as part of PX) has definitely become the norm in the field. In parallel, data re-use of public proteomics data has increased enormously, with multiple applications. We first describe the new architecture of PRIDE Archive, the archival component of PRIDE. PRIDE Archive and the related data submission framework have been further developed to support the increase in submitted data volumes and additional data types. A new scalable and fault tolerant storage backend, Application Programming Interface and web interface have been implemented, as a part of an ongoing process. Additionally, we emphasize the improved support for quantitative proteomics data through the mzTab format. At last, we outline key statistics on the current data contents and volume of downloads, and how PRIDE data are starting to be disseminated to added-value resources including Ensembl, UniProt and Expression Atlas.

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Language(s): eng - English
 Dates: 2018-112019-01
 Publication Status: Published in print
 Pages: 9
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: ISI: 000462587400064
DOI: 10.1093/nar/gky1106
 Degree: -

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Project name : European Union’s Horizon 2020 Research and Innovation Program
Grant ID : 686547
Funding program : Horizon 2020 (H2020)
Funding organization : European Commission (EC)

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Title: Nucleic Acids Research
  Other : Nucleic Acids Res.
Source Genre: Journal
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Publ. Info: -
Pages: - Volume / Issue: 47 (D1) Sequence Number: - Start / End Page: D442 - D450 Identifier: ISSN: 0301-5610
CoNE: https://pure.mpg.de/cone/journals/resource/1000000000262810